The primary mode of HIV transmission worldwide is by exposure to the virus at vaginal, rectal or oral mucosal surfaces. To understand HIV/SIV transmission events at mucosal portals of entry, we used the SIV:macaque model to determine if mucosal surfaces function as barriers and select for particular viral genotypes. Rhesus macaques were inoculated intravaginally, intracolonically, intrarectally, or orally with the complex primary viral isolate SIV/DeltaB670. Peripheral blood mononuclear cells, collected within the first two weeks postinoculation, were cloned and sequenced from all infected macaques. In the majority of the animals analyzed, multiple genotypes were identified, independent of the route of infection. These findings suggest that the mucosal barrier may play a minor role in the genotypic selection observed during sexual transmission of HIV and emphasize the need to evaluate the viral diversity present within the mucosal secretions of chronically infected individuals.